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IMP Reference Guide
2.15.0
The Integrative Modeling Platform
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Creates a restraint between two Gaussian Mixture Models, "model" and "density". More...
#include <IMP/bayesianem/GaussianEMRestraint.h>
Inheritance diagram for IMP::bayesianem::GaussianEMRestraint:Creates a restraint between two Gaussian Mixture Models, "model" and "density".
This restrains two sets of GMMs with a density overlap function. The function is correlation of the two GMMs \(f_M\) and \(f_D\):
\[ \frac{2\int{f_M(x)f_D(x)dx}}{\int{f_M^2(x)+f_D^2(x)dx}} \]
Where the integral is the "overlap function" given by:
\[ ov(f_M,f_D) = \sum_{i=1}^{N_M} \sum_{j=1}^{N_D} \frac{1}{(2 \pi)^{3/2}|\Sigma_{Mi}+\Sigma_{Dj}|^{1/2}}\exp\left [-\frac{1}{2}(\boldsymbol\mu_{Mi} - \boldsymbol\mu_{Dj})^\top (\Sigma_{Mi}+\Sigma_{Dj})^{-1} (\boldsymbol\mu_{Mi} - \boldsymbol \mu_{Dj})\right ] \]
Definition at line 77 of file bayesianem/GaussianEMRestraint.h.
Public Member Functions | |
| GaussianEMRestraint (Model *mdl, ParticleIndexes model_ps, ParticleIndexes density_ps, ParticleIndex global_sigma, Float model_cutoff_dist, Float density_cutoff_dist, Float slope, bool update_model=true, bool backbone_slope=false, std::string name="GaussianEMRestraint%1%") | |
| Setup the GaussianEMRestraint. More... | |
| void | compute_initial_scores () |
| Pre-calculate the density-density and model-model scores. More... | |
| void | debug () |
| virtual IMP::ModelObjectsTemp | do_get_inputs () const |
| RestraintInfo * | get_dynamic_info () const |
| ParticleIndexes const | get_indexes () |
| Floats const | get_log2 () |
| double | get_probability () const |
| Returns exp(score) More... | |
| Float | get_slope () |
| Get restraint slope. More... | |
| RestraintInfo * | get_static_info () const |
| virtual std::string | get_type_name () const |
| virtual ::IMP::VersionInfo | get_version_info () const |
| Get information about the module and version of the object. More... | |
| void | set_density_filename (std::string density_fn) |
| Set the filename corresponding to the density GMM particles. More... | |
| void | set_slope (Float s) |
| Set restraint slope. More... | |
| void | show (std::ostream &out) const |
| virtual double | unprotected_evaluate (IMP::DerivativeAccumulator *accum) const |
| Public Member Functions inherited from IMP::Restraint | |
| Restraint (Model *m, std::string name) | |
| void | add_score_and_derivatives (ScoreAccumulator sa) const |
| Perform the actual restraint scoring. More... | |
| Restraint * | create_current_decomposition () const |
| Decompose this restraint into constituent terms for the current conf. More... | |
| Restraint * | create_decomposition () const |
| Decompose this restraint into constituent terms. More... | |
| virtual ScoringFunction * | create_scoring_function (double weight=1.0, double max=NO_MAX) const |
| Create a scoring function with only this restraint. More... | |
| virtual double | get_last_score () const |
| double | get_score () const |
| bool | get_was_good () const |
| void | set_weight (Float weight) |
| Float | get_weight () const |
| double | get_maximum_score () const |
| void | set_maximum_score (double s) |
| Public Member Functions inherited from IMP::ModelObject | |
| ModelObject (Model *m, std::string name) | |
| bool | get_has_dependencies () const |
| Return whether this object has dependencies computed. More... | |
| bool | get_has_required_score_states () const |
| Return whether score states are computed. More... | |
| ModelObjectsTemp | get_inputs () const |
| ModelObjectsTemps | get_interactions () const |
| Get the interacting sets induced by this ModelObject. More... | |
| Model * | get_model () const |
| ModelObjectsTemp | get_outputs () const |
| const ScoreStatesTemp & | get_required_score_states () const |
| Get the score states that are ancestors of this in the dependency graph. More... | |
| void | set_has_dependencies (bool tf) |
| Either invalidate the dependencies or ensure they are correct. More... | |
| void | set_has_required_score_states (bool tf) |
| Compute the required score states. More... | |
| Public Member Functions inherited from IMP::Object | |
| virtual void | clear_caches () |
| CheckLevel | get_check_level () const |
| LogLevel | get_log_level () const |
| void | set_check_level (CheckLevel l) |
| void | set_log_level (LogLevel l) |
| Set the logging level used in this object. More... | |
| void | set_was_used (bool tf) const |
| void | show (std::ostream &out=std::cout) const |
| const std::string & | get_name () const |
| void | set_name (std::string name) |
Additional Inherited Members | |
| Protected Member Functions inherited from IMP::Restraint | |
| virtual void | do_add_score_and_derivatives (ScoreAccumulator sa) const |
| A restraint should override this to compute the score and derivatives. More... | |
| virtual Restraints | do_create_current_decomposition () const |
| virtual Restraints | do_create_decomposition () const |
| ModelObjectsTemp | do_get_outputs () const |
| Protected Member Functions inherited from IMP::ModelObject | |
| virtual ModelObjectsTemps | do_get_interactions () const |
| virtual void | handle_set_has_required_score_states (bool) |
| Protected Member Functions inherited from IMP::Object | |
| Object (std::string name) | |
| Construct an object with the given name. More... | |
| virtual void | do_destroy () |
| IMP::bayesianem::GaussianEMRestraint::GaussianEMRestraint | ( | Model * | mdl, |
| ParticleIndexes | model_ps, | ||
| ParticleIndexes | density_ps, | ||
| ParticleIndex | global_sigma, | ||
| Float | model_cutoff_dist, | ||
| Float | density_cutoff_dist, | ||
| Float | slope, | ||
| bool | update_model = true, |
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| bool | backbone_slope = false, |
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| std::string | name = "GaussianEMRestraint%1%" |
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| ) |
Setup the GaussianEMRestraint.
| [in] | mdl | the Model object to operate on |
| [in] | model_ps | particles for the model GMM |
| [in] | density_ps | particles for the density GMM |
| [in] | global_sigma | Particle to modulate the uncertainty |
| [in] | model_cutoff_dist | Cutoff for the model-model interactions |
| [in] | density_cutoff_dist | Cutoff for model-density interactions |
| [in] | slope | Gentle term to move all particles to the density |
| [in] | update_model | (DEPRECATED) update model each cycle |
| [in] | backbone_slope | Limit the slope only to backbone particles |
| [in] | name | Name of this restraint |
| void IMP::bayesianem::GaussianEMRestraint::compute_initial_scores | ( | ) |
Pre-calculate the density-density and model-model scores.
This is automatically called by the constructor. You only need to call it manually if you change Gaussian variances
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Get any Particle, Container or other ModelObjects read by this during evaluation. If you read everything in a container, you can just return that container.
Implements IMP::ModelObject.
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Reimplemented from IMP::Restraint.
| double IMP::bayesianem::GaussianEMRestraint::get_probability | ( | ) | const |
Returns exp(score)
Definition at line 103 of file bayesianem/GaussianEMRestraint.h.
| Float IMP::bayesianem::GaussianEMRestraint::get_slope | ( | ) |
Get restraint slope.
Definition at line 134 of file bayesianem/GaussianEMRestraint.h.
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virtual |
Reimplemented from IMP::Restraint.
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Get information about the module and version of the object.
Reimplemented from IMP::Object.
Definition at line 148 of file bayesianem/GaussianEMRestraint.h.
| void IMP::bayesianem::GaussianEMRestraint::set_density_filename | ( | std::string | density_fn | ) |
Set the filename corresponding to the density GMM particles.
If the density GMM particles were read from a file, this method can be used to tell the restraint so that it can track this information back to the original EM density file, which is useful for deposition.
Definition at line 112 of file bayesianem/GaussianEMRestraint.h.
Here is the call graph for this function:| void IMP::bayesianem::GaussianEMRestraint::set_slope | ( | Float | s | ) |
Set restraint slope.
Definition at line 131 of file bayesianem/GaussianEMRestraint.h.